def set_meta( self, dataset, **kwd ): """ for lped/pbed eg """ Html.set_meta( self, dataset, **kwd ) if kwd.get('overwrite') == False: return True try: efp = dataset.extra_files_path except: return False try: flist = os.listdir(efp) except: return False if len(flist) == 0: return False self.regenerate_primary_file(dataset) if not dataset.info: dataset.info = 'Galaxy Impute2 datatype object' if not dataset.blurb: dataset.blurb = 'Composite file - Otago Impute2 Galaxy toolkit' return True
def set_meta( self, dataset, **kwd ): """ for lped/pbed eg """ Html.set_meta( self, dataset, **kwd ) if kwd.get('overwrite') == False: if verbose: gal_Log.debug('@@@ rgenetics set_meta called with overwrite = False') return True try: efp = dataset.extra_files_path except: if verbose: gal_Log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.name)) return False try: flist = os.listdir(efp) except: if verbose: gal_Log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0],dataset.name)) return False if len(flist) == 0: if verbose: gal_Log.debug('@@@rgenetics set_meta failed - %s efp %s is empty?' % (dataset.name,efp)) return False self.regenerate_primary_file(dataset) if not dataset.info: dataset.info = 'Galaxy genotype datatype object' if not dataset.blurb: dataset.blurb = 'Composite file - Rgenetics Galaxy toolkit' return True
def set_meta(self, dataset, **kwd): Html.set_meta(self, dataset, **kwd) efp = dataset.extra_files_path flist = os.listdir(efp) for i, fname in enumerate(flist): if fname.endswith('.grp'): dataset.metadata.reference_name = fname[:-4] break self.regenerate_primary_file(dataset)
def __init__(self, **kwd): Html.__init__(self, **kwd) self.add_composite_file('%s.ped', description='Pedigree File', substitute_name_with_metadata='base_name', is_binary=False) self.add_composite_file('%s.map', description='Map File', substitute_name_with_metadata='base_name', is_binary=False)
def __init__(self, **kwd): Html.__init__( self, **kwd ) #self.add_composite_file('tagInfo.txt', description = 'basic configuration information', mimetype = 'text/html') # Contains basic configuration information self.add_composite_file('tagLengthDistribution.txt', description = 'histogram of read lengths used for alignment', mimetype = 'text/html') # File contains a histogram of read lengths used for alignment. self.add_composite_file('tagCountDistribution.txt', description = 'histogram of clonal read depth, showing the number of reads per unique position', mimetype = 'text/html') # File contains a histogram of clonal read depth, showing the number of reads per unique position. self.add_composite_file('tagAutocorrelation.txt', description = 'distribution of distances between adjacent reads in the genome', mimetype = 'text/html') # The autocorrelation routine creates a distribution of distances between adjacent reads in the genome. self.add_composite_file('tagFreq.txt', description = "nucleotide and dinucleotide frequencies as a function of distance from the 5' end of all reads", mimetype = 'text/html', optional=True) # Calculates the nucleotide and dinucleotide frequencies as a function of distance from the 5' end of all reads. self.add_composite_file('tagFreqUniq.txt', description = "nucleotide and dinucleotide frequencies as a function of distance from the 5' end of all reads (counted only once)", mimetype = 'text/html', optional=True) # Same as tagFreq.txt, however individual genomic positions are only counted once. self.add_composite_file('tagGCcontent.txt', description = 'Distribution of fragment GC%-content', mimetype = 'text/html', optional=True) # Distribution of fragment GC%-content. self.add_composite_file('genomeGCcontent.txt', description = 'Distribution of fragment GC%-content at each location in the genome', mimetype = 'text/html', optional=True) # Distribution of fragment GC%-content at each location in the genome.
def __init__(self, **kwd): Html.__init__(self, **kwd) log.debug("######### FUSION INSPECTOR DATA ############\n\n\n") #sys.exit(1) self.add_composite_file('FInspector.fusion_predictions.txt', description='fusion predictions', is_binary=False) self.add_composite_file('FInspector.fa', description='fusion contigs', mimetype='text/html', is_binary=False) self.add_composite_file('FInspector.fa.fai', description='fusion contigs index', is_binary=False) self.add_composite_file("FInspector.fusion_predictions.txt", description="fusion predictions summary", is_binary=False) self.add_composite_file("FInspector.igv.FusionJuncSpan", description="fusion support for IGV viewing", is_binary=False) self.add_composite_file("FInspector.consolidated.cSorted.bam", description="all fusion-supporting reads", is_binary=True) self.add_composite_file("FInspector.consolidated.cSorted.bam.bai", description="bam index", is_binary=True) self.add_composite_file( "FInspector.junction_reads.bam.bed.sorted.bed.gz", description="junction reads in bed.gz format", is_binary=True) self.add_composite_file( "FInspector.junction_reads.bam.bed.sorted.bed.gz.tbi", description="tabix index for junction reads bed.gz", is_binary=True) self.add_composite_file( "FInspector.spanning_reads.bam.bed.sorted.bed.gz", description="spanning reads in bed.gz format", is_binary=True) self.add_composite_file( "FInspector.spanning_reads.bam.bed.sorted.bed.gz.tbi", description="tabix index for spanning reads bed.gz", is_binary=True) self.add_composite_file( "FInspector.gmap_trinity_GG.fusions.gff3.bed.sorted.bed.gz", description="Trinity fusion transcript structures", is_binary=True) self.add_composite_file( "FInspector.gmap_trinity_GG.fusions.gff3.bed.sorted.bed.gz.tbi", description= "tabix index for trinity fusion transcript structures in bed.gz", is_binary=True)
def set_meta(self, dataset, **kwd): """ NOTE we apply the tabular machinary to the phenodata extracted from a BioC eSet or affybatch. """ Html.set_meta(self, dataset, **kwd) try: flist = os.listdir(dataset.extra_files_path) except: if verbose: gal_Log.debug('@@@rexpression set_meta failed - no dataset?') return False bn = dataset.metadata.base_name if not bn: for f in flist: n = os.path.splitext(f)[0] bn = n dataset.metadata.base_name = bn if not bn: bn = '?' dataset.metadata.base_name = bn pn = '%s.pheno' % (bn) pp = os.path.join(dataset.extra_files_path, pn) dataset.metadata.pheno_path = pp try: pf = file(pp, 'r').readlines( ) # read the basename.phenodata in the extra_files_path except: pf = None if pf: h = pf[0].strip() h = h.split('\t') # hope is header h = [escape(x) for x in h] dataset.metadata.column_names = h dataset.metadata.columns = len(h) dataset.peek = ''.join(pf[:5]) else: dataset.metadata.column_names = [] dataset.metadata.columns = 0 dataset.peek = 'No pheno file found' if pf and len(pf) > 1: dataset.metadata.pheCols = self.get_phecols(phenolist=pf) else: dataset.metadata.pheCols = [ ('', 'No useable phenotypes found', False), ] #self.regenerate_primary_file(dataset) if not dataset.info: dataset.info = 'Galaxy Expression datatype object' if not dataset.blurb: dataset.blurb = 'R loadable BioC expression object for the Rexpression Galaxy toolkit' return True
def set_meta( self, dataset, **kwd ): """ NOTE we apply the tabular machinary to the phenodata extracted from a BioC eSet or affybatch. """ Html.set_meta(self, dataset, **kwd) try: flist = os.listdir(dataset.extra_files_path) except: if verbose: gal_Log.debug('@@@rexpression set_meta failed - no dataset?') return False bn = dataset.metadata.base_name if not bn: for f in flist: n = os.path.splitext(f)[0] bn = n dataset.metadata.base_name = bn if not bn: bn = '?' dataset.metadata.base_name = bn pn = '%s.pheno' % (bn) pp = os.path.join(dataset.extra_files_path,pn) dataset.metadata.pheno_path=pp try: pf = file(pp,'r').readlines() # read the basename.phenodata in the extra_files_path except: pf = None if pf: h = pf[0].strip() h = h.split('\t') # hope is header h = [escape(x) for x in h] dataset.metadata.column_names = h dataset.metadata.columns = len(h) dataset.peek = ''.join(pf[:5]) else: dataset.metadata.column_names = [] dataset.metadata.columns = 0 dataset.peek = 'No pheno file found' if pf and len(pf) > 1: dataset.metadata.pheCols = self.get_phecols(phenolist=pf) else: dataset.metadata.pheCols = [('','No useable phenotypes found',False),] #self.regenerate_primary_file(dataset) if not dataset.info: dataset.info = 'Galaxy Expression datatype object' if not dataset.blurb: dataset.blurb = 'R loadable BioC expression object for the Rexpression Galaxy toolkit' return True
def __init__(self, **kwd): Html.__init__(self, **kwd) self.add_composite_file('Sequences', mimetype='text/html', description='Sequences', substitute_name_with_metadata=None, is_binary=False) self.add_composite_file('Roadmaps', mimetype='text/html', description='Roadmaps', substitute_name_with_metadata=None, is_binary=False) self.add_composite_file('Log', mimetype='text/html', description='Log', optional='True', substitute_name_with_metadata=None, is_binary=False)
def __init__( self, **kwd ): Html.__init__( self, **kwd ) log.debug("######### FUSION INSPECTOR DATA ############\n\n\n") #sys.exit(1) self.add_composite_file('FInspector.fusion_predictions.txt', description = 'fusion predictions', is_binary = False ) self.add_composite_file('FInspector.fa', description = 'fusion contigs', mimetype = 'text/html', is_binary = False ) self.add_composite_file('FInspector.fa.fai', description = 'fusion contigs index', is_binary = False ) self.add_composite_file("FInspector.fusion_predictions.txt", description="fusion predictions summary", is_binary=False) self.add_composite_file("FInspector.igv.FusionJuncSpan", description="fusion support for IGV viewing", is_binary=False) self.add_composite_file("FInspector.consolidated.cSorted.bam", description="all fusion-supporting reads", is_binary=True) self.add_composite_file("FInspector.consolidated.cSorted.bam.bai", description="bam index", is_binary=True) self.add_composite_file("FInspector.junction_reads.bam.bed.sorted.bed.gz", description="junction reads in bed.gz format", is_binary=True) self.add_composite_file("FInspector.junction_reads.bam.bed.sorted.bed.gz.tbi", description="tabix index for junction reads bed.gz", is_binary=True) self.add_composite_file("FInspector.spanning_reads.bam.bed.sorted.bed.gz", description="spanning reads in bed.gz format", is_binary=True) self.add_composite_file("FInspector.spanning_reads.bam.bed.sorted.bed.gz.tbi", description="tabix index for spanning reads bed.gz", is_binary=True) self.add_composite_file("FInspector.gmap_trinity_GG.fusions.gff3.bed.sorted.bed.gz", description="Trinity fusion transcript structures", is_binary=True) self.add_composite_file("FInspector.gmap_trinity_GG.fusions.gff3.bed.sorted.bed.gz.tbi", description="tabix index for trinity fusion transcript structures in bed.gz", is_binary=True)
def __init__( self, **kwd ): Html.__init__( self, **kwd ) self.add_composite_file('run.info', description = 'run.info', mimetype = 'text/html', optional = True, is_binary = False ) self.add_composite_file('read_groups.info', description = 'read_groups.info', mimetype = 'text/html', optional = True, is_binary = False ) self.add_composite_file('cds.count_tracking', description = 'cds.count_tracking', mimetype = 'text/html', optional = True, is_binary = False ) self.add_composite_file('cds.diff', description = 'cds.diff', mimetype = 'text/html', optional = True, is_binary = False ) self.add_composite_file('cds.fpkm_tracking', description = 'cds.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False ) self.add_composite_file('cds.read_group_tracking', description = 'cds.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False ) self.add_composite_file('cds_exp.diff', description = 'cds_exp.diff', mimetype = 'text/html', optional = True, is_binary = False ) self.add_composite_file('gene_exp.diff', description = 'gene_exp.diff', mimetype = 'text/html', optional = True, is_binary = False ) self.add_composite_file('genes.count_tracking', description = 'genes.count_tracking', mimetype = 'text/html', optional = True, is_binary = False ) self.add_composite_file('genes.fpkm_tracking', description = 'genes.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False ) self.add_composite_file('genes.read_group_tracking', description = 'genes.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False ) self.add_composite_file('isoform_exp.diff', description = 'isoform_exp.diff', mimetype = 'text/html', optional = True, is_binary = False ) self.add_composite_file('isoforms.count_tracking', description = 'isoforms.count_tracking', mimetype = 'text/html', optional = True, is_binary = False ) self.add_composite_file('isoforms.fpkm_tracking', description = 'isoforms.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False ) self.add_composite_file('isoforms.read_group_tracking', description = 'isoforms.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False ) self.add_composite_file('promoters.diff', description = 'promoters.diff', mimetype = 'text/html', optional = True, is_binary = False ) self.add_composite_file('splicing.diff', description = 'splicing.diff', mimetype = 'text/html', optional = True, is_binary = False ) self.add_composite_file('tss_group_exp.diff', description = 'tss_group_exp.diff', mimetype = 'text/html', optional = True, is_binary = False ) self.add_composite_file('tss_groups.count_tracking', description = 'tss_groups.count_tracking', mimetype = 'text/html', optional = True, is_binary = False ) self.add_composite_file('tss_groups.fpkm_tracking', description = 'tss_groups.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False ) self.add_composite_file('tss_groups.read_group_tracking', description = 'tss_groups.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
def __init__(self, **kwd): Html.__init__(self, **kwd) self.add_composite_file( "Sequences", mimetype="text/html", description="Sequences", substitute_name_with_metadata=None, is_binary=False, ) self.add_composite_file( "Roadmaps", mimetype="text/html", description="Roadmaps", substitute_name_with_metadata=None, is_binary=False, ) self.add_composite_file( "Log", mimetype="text/html", description="Log", optional="True", substitute_name_with_metadata=None, is_binary=False, )
def __init__( self, **kwd ): Html.__init__( self, **kwd ) self.add_composite_file( 'Sequences', mimetype='text/html', description='Sequences', substitute_name_with_metadata=None, is_binary=False ) self.add_composite_file( 'Roadmaps', mimetype='text/html', description='Roadmaps', substitute_name_with_metadata=None, is_binary=False ) self.add_composite_file( 'Log', mimetype='text/html', description='Log', optional='True', substitute_name_with_metadata=None, is_binary=False )
def __init__( self, **kwd ): Html.__init__(self,**kwd) self.add_composite_file( '%s.pheno', description = 'Phenodata tab text file', substitute_name_with_metadata = 'base_name', is_binary=False)
def __init__(self, **kwd): Html.__init__(self, **kwd) self.add_composite_file('run.info', description='run.info', mimetype='text/html', optional=True, is_binary=False) self.add_composite_file('read_groups.info', description='read_groups.info', mimetype='text/html', optional=True, is_binary=False) self.add_composite_file('cds.count_tracking', description='cds.count_tracking', mimetype='text/html', optional=True, is_binary=False) self.add_composite_file('cds.diff', description='cds.diff', mimetype='text/html', optional=True, is_binary=False) self.add_composite_file('cds.fpkm_tracking', description='cds.fpkm_tracking', mimetype='text/html', optional=True, is_binary=False) self.add_composite_file('cds.read_group_tracking', description='cds.read_group_tracking', mimetype='text/html', optional=True, is_binary=False) self.add_composite_file('cds_exp.diff', description='cds_exp.diff', mimetype='text/html', optional=True, is_binary=False) self.add_composite_file('gene_exp.diff', description='gene_exp.diff', mimetype='text/html', optional=True, is_binary=False) self.add_composite_file('genes.count_tracking', description='genes.count_tracking', mimetype='text/html', optional=True, is_binary=False) self.add_composite_file('genes.fpkm_tracking', description='genes.fpkm_tracking', mimetype='text/html', optional=True, is_binary=False) self.add_composite_file('genes.read_group_tracking', description='genes.read_group_tracking', mimetype='text/html', optional=True, is_binary=False) self.add_composite_file('isoform_exp.diff', description='isoform_exp.diff', mimetype='text/html', optional=True, is_binary=False) self.add_composite_file('isoforms.count_tracking', description='isoforms.count_tracking', mimetype='text/html', optional=True, is_binary=False) self.add_composite_file('isoforms.fpkm_tracking', description='isoforms.fpkm_tracking', mimetype='text/html', optional=True, is_binary=False) self.add_composite_file('isoforms.read_group_tracking', description='isoforms.read_group_tracking', mimetype='text/html', optional=True, is_binary=False) self.add_composite_file('promoters.diff', description='promoters.diff', mimetype='text/html', optional=True, is_binary=False) self.add_composite_file('splicing.diff', description='splicing.diff', mimetype='text/html', optional=True, is_binary=False) self.add_composite_file('tss_group_exp.diff', description='tss_group_exp.diff', mimetype='text/html', optional=True, is_binary=False) self.add_composite_file('tss_groups.count_tracking', description='tss_groups.count_tracking', mimetype='text/html', optional=True, is_binary=False) self.add_composite_file('tss_groups.fpkm_tracking', description='tss_groups.fpkm_tracking', mimetype='text/html', optional=True, is_binary=False) self.add_composite_file('tss_groups.read_group_tracking', description='tss_groups.read_group_tracking', mimetype='text/html', optional=True, is_binary=False)
def set_meta( self, dataset, **kwd ): log.debug("## set_meta for FusionInspector ") Html.set_meta( self, dataset, **kwd ) self.regenerate_primary_file(dataset)
def set_meta( self, dataset, **kwd ): Html.set_meta( self, dataset, **kwd ) self.regenerate_primary_file(dataset)
def __init__(self, **kwd): Html.__init__(self, **kwd)
def __init__( self, **kwd ): Html.__init__( self, **kwd ) self.add_composite_file( '%s.ped', description = 'Pedigree File', substitute_name_with_metadata = 'base_name', is_binary = False ) self.add_composite_file( '%s.map', description = 'Map File', substitute_name_with_metadata = 'base_name', is_binary = False )
def __init__(self, **kwd): Html.__init__(self, **kwd) """ Expecting files: extra_files_path/<reference_name>.grp extra_files_path/<reference_name>.ti extra_files_path/<reference_name>.seq extra_files_path/<reference_name>.transcripts.fa Optionally includes files: extra_files_path/<reference_name>.chrlist extra_files_path/<reference_name>.idx.fa extra_files_path/<reference_name>.1.ebwt extra_files_path/<reference_name>.2.ebwt extra_files_path/<reference_name>.3.ebwt extra_files_path/<reference_name>.4.ebwt extra_files_path/<reference_name>.rev.1.ebwt extra_files_path/<reference_name>.rev.2.ebwt """ self.add_composite_file('%s.grp', description='Group File', substitute_name_with_metadata='reference_name', is_binary=False) self.add_composite_file('%s.ti', description='', substitute_name_with_metadata='reference_name', is_binary=False) self.add_composite_file('%s.seq', description='', substitute_name_with_metadata='reference_name', is_binary=False) self.add_composite_file('%s.transcripts.fa', description='', substitute_name_with_metadata='reference_name', is_binary=False) self.add_composite_file('%s.chrlist', description='', substitute_name_with_metadata='reference_name', is_binary=False, optional=True) self.add_composite_file('%s.idx.fa', description='', substitute_name_with_metadata='reference_name', is_binary=False, optional=True) self.add_composite_file('%s.1.ebwt', description='', substitute_name_with_metadata='reference_name', is_binary=True, optional=True) self.add_composite_file('%s.2.ebwt', description='', substitute_name_with_metadata='reference_name', is_binary=True, optional=True) self.add_composite_file('%s.3.ebwt', description='', substitute_name_with_metadata='reference_name', is_binary=True, optional=True) self.add_composite_file('%s.4.ebwt', description='', substitute_name_with_metadata='reference_name', is_binary=True, optional=True) self.add_composite_file('%s.rev.1.ebwt', description='', substitute_name_with_metadata='reference_name', is_binary=True, optional=True) self.add_composite_file('%s.rev.2.ebwt', description='', substitute_name_with_metadata='reference_name', is_binary=True, optional=True)
def __init__(self, **kwd): Html.__init__(self, **kwd) self.add_composite_file('%s.pheno', description='Phenodata tab text file', substitute_name_with_metadata='base_name', is_binary=True)
def set_meta(self, dataset, **kwd): log.debug("## set_meta for FusionInspector ") Html.set_meta(self, dataset, **kwd) self.regenerate_primary_file(dataset)